Assume that there are two users, user A and user B. At first, user A signs in Microsoft Skype for Business 2016 in a Citrix environment. Then user B signs in the client in a normal environment. In this situation, if user A sets the custom location, user B cannot see it. Then, if user A disconnects the Citrix Xendesktop (The client is still running on VM), user B can see the custom location.
This issue occurs because when you determine whether the location should be published, you only check whether the user is in VD1v1 or not.
To fix the issue, install the February 7, 2017, update (KB3141501) for Skype for Business 2016.